Variant report

Variant	rs1490384
Chromosome Location	chr6:126851160-126851161
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 76 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10457478	1.00[ASN][1000 genomes]
rs1155938	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1155939	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1159619	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12202204	1.00[ASN][1000 genomes]
rs1340952	0.85[EUR][1000 genomes]
rs1340953	0.86[EUR][1000 genomes]
rs1361108	1.00[ASN][1000 genomes]
rs1361262	1.00[ASN][1000 genomes]
rs1490385	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1490387	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1490388	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1538172	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1538956	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs1578060	1.00[ASN][1000 genomes]
rs1591805	1.00[ASN][1000 genomes]
rs1602278	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17754780	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1826189	0.96[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs1844593	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1907067	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2045258	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2050644	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2130603	0.84[EUR][1000 genomes]
rs2326387	1.00[ASN][1000 genomes]
rs34539692	1.00[ASN][1000 genomes]
rs3861455	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3905044	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4053271	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4243491	0.93[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs4339479	0.86[EUR][1000 genomes]
rs4380768	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4422634	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4626447	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4629707	0.87[EUR][1000 genomes]
rs4895807	1.00[ASN][1000 genomes]
rs4895808	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4895813	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs6907898	0.81[CEU][hapmap];1.00[CHB][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6911485	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs6913430	0.85[EUR][1000 genomes]
rs6919397	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6921183	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6925689	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7738135	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7738836	0.85[EUR][1000 genomes]
rs7743860	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs8180649	0.83[EUR][1000 genomes]
rs853961	0.92[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs853962	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs853965	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs853985	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs853986	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs853987	0.83[EUR][1000 genomes]
rs864937	0.84[EUR][1000 genomes]
rs864938	0.83[EUR][1000 genomes]
rs9321065	1.00[ASN][1000 genomes]
rs9375435	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9375442	0.89[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs9375446	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9375447	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9375450	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs9388486	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9388487	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9388489	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9388490	1.00[ASN][1000 genomes]
rs9388500	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9388507	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs9388509	0.84[EUR][1000 genomes]
rs9398803	1.00[ASN][1000 genomes]
rs9401876	0.86[AFR][1000 genomes]
rs9401885	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9401888	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9491624	1.00[CHB][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021636	chr6:126792916-127022489	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1026498	chr6:126812609-127397240	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

Variant related diseases (count:2)

Disease	PMID	Source
Height	23563607	GWAS catalog
Height	20881960	GWAS catalog

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:126848400-126852600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:126848400-126853000	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr6:126848400-126855200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr6:126848600-126853000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr6:126848600-126853200	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr6:126848600-126855800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr6:126849000-126855600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr6:126849600-126851200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr6:126850600-126851800	Enhancers	Stomach Mucosa	stomach
10	chr6:126850800-126851200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:126850800-126851200	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr6:126850800-126851200	Enhancers	Fetal Brain Male	brain
13	chr6:126850800-126851400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:126850800-126853400	Enhancers	Duodenum Mucosa	Duodenum
15	chr6:126850800-126854200	Enhancers	Fetal Intestine Large	intestine
16	chr6:126850800-126854200	Enhancers	Fetal Intestine Small	intestine
17	chr6:126851000-126852000	Enhancers	Duodenum Smooth Muscle	Duodenum
18	chr6:126851000-126852800	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr6:126851000-126853000	Enhancers	Rectal Mucosa Donor 29	rectum

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